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Assignment of parentage with molecular markers is most difficult when the true parents have close relatives in the adult population. Here, we present an efficient solution to that problem by extending simple exclusion approaches to parentage analysis with single nucleotide polymorphic markers (SNPs). We augmented the previously published homozygote opposite test (hot), which counts mismatches due to the offspring and candidate parent having different homozygous genotypes, with an additional test. In this case, parents homozygous for the same SNP are incompatible with heterozygous offspring (i.e., "Homozygous Identical Parents, Heterozygous Offspring are Precluded": hiphop). We tested this approach in a cooperatively breeding bird, the superb fairy-wren, Malurus cyaneus, where rates of extra-pair paternity are exceptionally high, and where paternity assignment is challenging because breeding males typically have first-order adult relatives in their neighbourhood. Combining the tests and conditioning on the maternal genotype with a set of 1376 autosomal SNPs always allowed us to distinguish a single most likely sire from his relatives, and also to identify cases where the true sire must have been unsampled. In contrast, if just the hot test was used, we failed to identify a single most-likely sire in 2.5% of cases. Resampling enabled us to create guidelines for the number of SNPs required when first-order relatives coexist in the mating pool. Our method, implemented in the R package hiphop, therefore provides unambiguous parentage assignments even in systems with complex social organisation. We also identified a suite of Z- and W-linked SNPs that always identified sex correctly., (© 2021 John Wiley & Sons Ltd.)

The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses., (© 2019 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

The extent of range overlap of incipient and recent species depends on the type and magnitude of phenotypic divergence that separates them, and the consequences of phenotypic divergence on their interactions. Signal divergence by social selection likely initiates many speciation events, but may yield niche-conserved lineages predisposed to limit each others' ranges via ecological competition. Here, we examine this neglected aspect of social selection speciation theory in relation to the discovery of a nonecotonal species border between sunbirds. We find that Nectarinia moreaui and Nectarinia fuelleborni meet in a ∼6 km wide contact zone, as estimated by molecular cline analysis. These species exploit similar bioclimatic niches, but sing highly divergent learned songs, consistent with divergence by social selection. Cline analyses suggest that within-species stabilizing social selection on song-learning predispositions maintains species differences in song despite both hybridization and cultural transmission. We conclude that ecological competition between moreaui and fuelleborni contributes to the stabilization of the species border, but that ecological competition acts in conjunction with reproductive interference. The evolutionary maintenance of learned song differences in a hybrid zone recommend this study system for future studies on the mechanisms of learned song divergence and its role in speciation., (© 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.)

Muscicapa flycatchers and their allies (Bradornis, Dioptornis, Empidornis, Fraseria, Myioparus, Namibornis, and Sigelus) are widely distributed in Africa, Europe and Asia. This broad distribution and the wide variety of habitats occupied by the group, ranging from arid to tropical forests, presents an interesting opportunity to explore the evolution of biogeographic patterns and habitat associations. Sequence data (up to 3310 base pairs from two mitochondrial and two nuclear genes) were generated for 36 of 42 species which comprise the assemblage. Complementary data from an additional species was retrieved from GenBank, as was an additional gene which was available for 21 of our included taxa. Using model-based phylogenetic methods and molecular clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the lineage. Ancestral area reconstructions were performed on the phylogeny using LaGrange and BioGeoBEARS. Our results indicate that Bradornis, Fraseria, and Muscicapa are each non-monophyletic, with the latter being shown to comprise five separate clades each more closely related to other genera. Two new genera (Chapinia and Ripleyia) are erected to account for these results. Muscicapa and allies originated c. 7.4 Ma, most likely in Africa given that their sister lineage is almost entirely from there, and rapidly achieved a Eurasian distribution by c. 7.1 Ma. A second divergence at c. 6.1 Ma resulted in two clades. The first is a largely Eurasian clade that subsequently recolonized Africa, perhaps as the result of the loss of migration. The second is an African clade, and ancestral reconstructions suggest a Congolian (e.g. tropical forest) origin for this clade, with several subsequent diversifications into more arid habitats. This is a unique result, as most tropical forest lineages are confined to that habitat. As with other studies of African bird lineages, Afrotropical forest dynamics appear to have played a significant role in driving diversification in Muscicapa and allies, and our results include just the second recorded case of southern to northern African colonization patterns., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Erythropygia scrub-robins and their allies are distributed throughout Africa, Europe, Southeast Asia, India, Madagascar and the Seychelles. This broad distribution, as well as the distribution of Erythropygia taxa across Africa, presents an interesting opportunity to explore the mechanisms by which this biogeographic distribution was achieved. Multilocus sequence data (3310 base pairs from two mitochondrial and two nuclear genes) were generated for all species of Erythropygia and Cercotrichas scrub-robins, as well as from genera previously shown to render Erythropygia paraphyletic. Using model-based phylogenetic methods and molecular clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the lineage. Ancestral area reconstructions were performed on the phylogeny using probabilistic approaches implemented in LaGrange and BioGeoBEARS. Our results confirm that Erythropygia is not monophyletic, and that one of the two Erythropygia clades is more closely related to a clade of Asian and Indian Ocean islands distributed species. Overall, the Erythropygia and allies clade originated in Africa in the late Miocene c. 6.9 Ma. Subsequently, a number of overwater dispersals occurred to include an initial colonization of Southeast Asia, and an ensuing progression of colonizations from Southeast Asia to the Seychelles, from there to Madagascar, and from these Indian Ocean islands back to Southeast Asia. Within the two clades of Erythropygia, ancestral area reconstructions within Africa indicate a Southern Africa origin, with subsequent lineage divergence in each clade indicating northward colonization. Overall, this clade of non-migratory songbirds shows a remarkable number of trans-oceanic colonization events, that were possibly facilitated by wind-driven dispersal; repeated Africa to Asia colonizations, two of which occur in this clade, are exceptionally rare in birds. Also rare is our finding that colonization patterns in Africa indicate a southern to northern progression., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Learned traits are thought to be subject to different evolutionary dynamics than other phenotypes, but their evolutionary tempo and mode has received little attention. Learned bird song has been thought to be subject to rapid and constant evolution. However, we know little about the evolutionary modes of learned song divergence over long timescales. Here, we provide evidence that aspects of the territorial songs of Eastern Afromontane sky island sunbirds Cinnyris evolve in a punctuated fashion, with periods of stasis of the order of hundreds of thousands of years or more, broken up by evolutionary pulses. Stasis in learned songs is inconsistent with learned traits being subject to constant or frequent change, as would be expected if selection does not constrain song phenotypes over evolutionary timescales. Learned song may instead follow a process resembling peak shifts on adaptive landscapes. While much research has focused on the potential for rapid evolution in bird song, our results suggest that selection can tightly constrain the evolution of learned songs over long timescales. More broadly, these results demonstrate that some aspects of highly variable, plastic traits can exhibit punctuated evolution, with stasis over long time periods. [ABSTRACT FROM AUTHOR]